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Sunday, February 27, 2011

There seems to be a trend amongst 'western' geneticists, to cite third party (not of their own) sources to bolster theories that cannot be sufficiently explained by their own findings. This often leads to the referencing of sources that concern samples of geographic specifics, and possibly, sample sizes that are distinct from those of the research group doing the citing [of the foreign source], without full understanding of the archeological record and linguistic background of the sample subjects under study. A good example of this can be found in the 2009 study by Tishkoff et al. that was the topic of this blog in the same year, wherein the authors cite at least three different external sources on Fulani gene pool, concerning Y-DNA, mtDNA, and lactase persistence-affiliated T-13910 allele of the MCM6 gene, as means of securing support for a theory they envisioned from their limited data. For instance, they speculated that a section of their Fulani samples must have low to moderate levels of "European/Middle Eastern" ancestry, because there was some connection with the "European/Middle Eastern" cluster. Apparently their results were not sufficient enough to make that speculation conclusive, and so, compelled them to call on external sources as means to buttress their estimation of their results.
As another example, let's take Arnaiz-Villena et al. (2001), whereby they had to rely on third party sample DNA findings to supplement their own evaluations. Now because they had relied heavily on third party sources on certain haplotype information for certain population samples, they were restricted from making direct comparisons between those samples and other samples from other studies, including their very own, using designated haplotypes that they used on their own samples but that were not tested by the third party sources. See:

Two types of analyses were carried out to compare Macedonian HLA frequencies with other Mediterranean population frequencies: 1) with DRB1 data, which is probably a more informative and discriminating methodology; and 2) with generic (low-resolution) DR-DQ data. These two types of analysis were both performed because some of the populations used for comparison lacked HLA-A and -B data [Berbers (from Souss, Agadir area, Morocco), Jews (Ashkenazi), Jews (Morocco), Jews (non-Ashkenazi), Lebanese (NS and KZ), see Table 1], or high resolution HLA-DQ data [(Greeks (Attica), Greeks (Cyprus), Greeks (Attica-Aegean), see Table 1]], or only generic HLA-DR and -DQ datawere available [Portuguese, Turks, Iranians, Armenians and Egyptians, see Table 1].

Had Arnaiz-Villena et al. (2001) sampled these populations themselves rather than rely on third party produced data, they would have been able to make the sort of comparisons with the sort of markers that they couldn't do due to paucity of third party-sourced data, however logistically hideous such an undertaking could have been.

Additionally, third party-sourced data may not necessarily always have one-on-one compatibility with the samples of a present research team, that many researchers feel compelled to make, so as to draw conclusions about populations, even if their respective samples were presumably drawn from the same general geographical area and/or ethnic group. Sections of populations can and do have different histories, and so, caution must be undertaken to draw parallels between two sample sets studied by two different research teams. Many times however, researchers ignore meticulously exploring background information of third party-sampled specimens, perhaps because it is time consuming, and proceed onto make parallels between their own sample set, i.e. if they have one, and those of another research team and far-reaching conclusions about an ethnic group or nationality anyway, presumably grounded on the idea that said studies involve the same ethnic group and/or country (nationality).

Studies like the Tishkoff & Co. example just given (above), run into these sort of problems, because of their heavy reliance on unpredictable, and at times, homoplasic-prone loci of the genome [e.g. some indel or microsatellite loci of nuclear DNA, as well as hypervariable segments of mitochondrial DNA], that are inherited biparentally in the case of nuclear DNA, and have a propensity for churning out ambiguous or not well-definable results. These sort of studies therefore require reference to external sources that relied on non-recombining uniparentally-inherited loci which are more precise in their ramifications. And because the uniparental nuclear DNA of their own samples were not identified, divulged or isolated, the authors could not ascertain that the particular samples they were working with had the same background as those of the cited external references, and hence held hostage by mere guesswork about what they may be seeing in their study. Against this backdrop, we have research teams that rely on studies like the one below, which too use loci that are imprecise when it comes to tracking down the likely geographic origin of the marker under study, i.e. short of speculating based on frequency distributions of the genotype. For instance, the T allele mentioned in the abstract below has been named a "European" polymorphism by several authors based on little more than the reasoning that it is very common in Europe and less so elsewhere. These sort of loci are unlike the non-recombining loci of nuclear and mitochondrial DNA, in that single base substitutions and other polymorphisms replace preexisting nucleotide with high probability risks of loosing a comprehensive record of previous mutational events, because of recurrent recombination events ...

Lactase persistence genotypes and malaria susceptibility in Fulani of Mali.

Malar J. 2011 Jan 14

ABSTRACT:

BACKGROUND: Fulani are a widely spread African ethnic group characterized by lower susceptibility to Plasmodium falciparum, clinical malaria morbidity and higher rate of lactase persistence compared to sympatric tribes. Lactase non-persistence, often called lactose intolerance, is the normal condition where lactase activity in the intestinal wall declines after weaning. Lactase persistence, common in Europe, and in certain African people with traditions of raising cattle, is caused by polymorphisms in the enhancer region approximately 14 kb upstream of the lactase gene.

METHODS: To evaluate the relationship between malaria and lactase persistence genotypes, a 400 bp region surrounding the main European C/T-13910 polymorphism upstream of the lactase gene was sequenced. DNA samples used in the study originated from 162 Fulani and 79 Dogon individuals from Mali.

RESULTS: Among 79 Dogon only one heterozygote of the lactase enhancer polymorphism was detected, whereas all others were homozygous for the ancestral C allele. Among the Fulani, the main European polymorphism at locus C/T-13910 was by far the most common polymorphism, with an allele frequency of 37%. Three other single-nucleotide polymorphisms were found with allele frequencies of 3.7%, 1.9% and 0.6% each. The novel DNA polymorphism T/C-13906 was seen in six heterozygous Fulani. Among the Fulani with lactase non-persistence CC genotypes at the C/T-13910 locus, 24% had malaria parasites detectable by microscopy compared to 18% for lactase persistent genotypes (P = 0.29). Pooling the lactase enhancer polymorphisms to a common presumptive genotype gave 28% microscopy positives for non-persistent and 17% for others (P = 0.11).

CONCLUSIONS: Plasmodium falciparum parasitaemia in asymptomatic Fulani is more common in individuals with lactase non-persistence genotypes, but this difference is not statistically significant. The potential immunoprotective properties of dietary cow milk as a reason for the partial malaria resistance of Fulani warrant further investigation. - Ends

The only dedicated effort that comes to mind, with regards to reconstructing the phylogenetic background of lactase persistence-affiliated alleles, involves undertaking a geographically wide sampling, thereby ascertaining the allele types in the regions covered, and then proceeding to examine the arrangement of haplotypes flanking the LP (Lactase persistence) alleles in question. This is reminiscent of the procedure used by Nabil et al.(2007). These authors sequenced the haplotypes flanking the T allele, covering some 800 kb, including the sequencing of the entire 3,435 bp intron 13 of the MCM6 gene, reportedly to gauge whether the T allele could be the product of a recombination event, because best assurance of a convergent evolution scenario for the T allele and other LP-linked alleles from the background of different nucleotide clusters is contingent on the absence of transmission via recombination. Putting things into perspective, it is worth noting that although the T-13910 sequence is the allele commonly associated with LP trait, it is not the only allele linked to LP even in Europe. Nabil et al. themselves acknowledge this, and even in the case of the T-13910 variant, Nabil et al.'s tables demonstrate that many of the populations sampled had more than one allelelic background linked to the LP. The Fulani are no exception.

Click on the image for greater resolution.

Nabil et al. claim that T-13910 allele emerged multiple times on different nucleotide cluster arrangements, but then, that the one on the H98 haplotype likely emerged only once. They proclaim that they think this, because the nucleotide clusters of haplotype 87 (H87) look to be the foundational state upon which mutations leading to haplotype 98 (H98) likely emerged. However, inspection of nucleotide information provided by these authors themselves indicate that the nucleotide sequences of both haplotype 95 (H95) and haplotype 87 (H87) could just as well serve as the ancestral sequences for haplotype 98. Alas they ruled haplotype 95 out, presumably because 3 out of 6 individuals carrying haplotype 95 did not have the complete set of the relatively familiar sequences of SNP markers flanking the locus where the T-13910 allele lies, towards the 3' end of the DNA segment. Even though Nabil et al. supposed that haplotype 95's flanking "haplotype block" isn't as stable as that of haplotype 87, this does not strip it off chances to serve as a "foundational block" for the common haplotype 98. It could just as well emerge on the haplotypes like those of the remaining three sampling candidates for example, whom after all, shared the complete block of the more familiar haplotype 95 SNP/nucleotide clusters. So, while the contrasts in the flanking "haplotype blocks" of the studied haplotype 95 samples suggest it's flanking haplotype cluster arrangement is less stable than that of haplotype 87, there is indication that some degree of linkage disequilibrium (LD) still exists within the haplotype (H95) , albeit weaker than that observed for haplotype 87 (H87). So, as it turns out, while it may not necessarily apply to every LCT-affiliated flanking haplotype cluster, those LCT regions bearing the LP alleles—and possibly under selective pressure—could very well be in LD to some degree or another, thereby preserving records of mutational history that would otherwise be lost from recombination. This feature potentially reduces the unpredictability of those LCT regions under possible selective pressure, to the extent that one wants to reconstruct the most plausible phylogenetic backgrounds of would-be LP haplotypes; something that could otherwise prove to be an uphill battle, when working with regular or common LCT-associated haplotypes.

On another note, this is how the present author (blog author) looks at it: If T-13910 could emerge on different allelic backgrounds, then it could just as well emerge more than once in distinct populations with similar allelic ancestral backgrounds for the LCT and MCM6 genes; who's to say that it can't?! Just going off the schematic that Nabil et al. provide on the different haplotypes, all that is fundamentally necessary for T-13910 allele to emerge, is having haplotype 84 around, which if it were to undergo a C->T mutation on the MCM6 gene at 14kb upstream the LCT gene, and then another mutation down the road, at say, G->A 22kb upstream the LCT gene [and not necessarily in that order], would provide an allelic basis for haplotype 98 to emerge. The point is, that there are sufficient windows of opportunity available for the likes of haplotype 98, haplotype 48, haplotype 49 and 97 to emerge from distinct haplotype cluster backgrounds; heck, another group of haplotypes—with highly divergent backgrounds from those of haplotype 98 and the other just-mentioned haplotypes—carry the T allele. Now, because these authors too ultimately find their results insufficient to explain their preferred theory of non-European groups—like Fulani—having attained lactase persistent trait from Europeans, as opposed to convergent evolution, they too were compelled to cite an external source, as means to solidify their theory. Citing external sources in of itself is not an unreasonable thing to do; the only problem is that this source does not prove to be compelling. This is what they refer their readers to:

HLA class I in three West African ethnic groups: genetic distances from sub-Saharan and Caucasoid populations.

Fulani of Burkina Faso (West Africa) are a particularly interesting ethnic group because of their lower susceptibility to Plasmodium falciparum malaria as compared to sympatric populations, Mossi and Rimaibé. Moreover, the occurrence of a Caucasoid component in their genetic make-up has been suggested on the basis of their physical traits and cultural traditions even though this view was not supported by genetic studies. A total of 149 unrelated subjects (53 Mossi, 47 Rimaibé and 49 Fulani) have been typed for 97 HLA class I alleles with the amplification refractory mutation system/polymerase chain reaction (ARMS/PCR) technique. Mossi and Rimaibé data were pooled since none of the 42 statistically testable alleles exhibited a significant heterogeneity. These pooled gene frequencies were found to be very different from those of Fulani: a certain (P less than 0.001) or a likely (0.001 less than P less than 0.01) difference was found for 5 and 12 alleles, respectively. Four alleles (A*24, A*29, B*27, B*3701) appeared to be essentially "private" Fulani alleles with respect to the other two populations but their presence was not associated with higher resistance to P. falciparum. Our data have then been compared using chord distances (CD) with those from the literature on Africans (including Gambian Fulani) and Caucasoids. The Burkina Faso and Gambian Fulani turned out to be very different (CD=2.191). Moreover, Burkina Faso Fulani were very distant from sympatric Mossi and Rimaibé (CDs=1.912 and 1.884), whereas Gambian Fulani were similar to sympatric Mandinka and Wolof (CDs=0.412 and 0.388) to an extent comparable to that found between Mossi and Rimaibé (CD=0.555). Our study does not suggest the involvement of HLA I in the higher resistance to malaria of Fulani, and confirms a low, if any, Caucasoid component in their gene pool. - Ends

Nabil & Co. latched onto this report about a measly "caucasoid" element, i.e. if it can even be considered that—as per the authors' own words, to suggest that their fragile theory is on very solid ground. Speaking of "caucasoid", undoubtedly an outdated concept, we are told in the above abstract that "occurrence of a Caucasoid component in their genetic make-up has been suggested on the basis of their physical traits and cultural traditions even though this view was not supported by genetic studies." One has to wonder what indigenous Fulani culture on this green earth could possibly qualify as "caucasoid culture"; could it be pastoralism; dancing, Fula language? We will never quite be clear on the answer to this, because its Eurocentric proponents are predictably mute on the answer, leaving the rest of us to just keep wondering about possible answers. Nabil et al. themselves are guilty of dubiously using the term "Caucasian" in a taxonomic sense, as if to declare European "ownership" of the allele in question.

It should be noted that of the four methods used by Nabil & Co. in estimating the MRCA ages, only three have been applied on Fulani samples. The Fulani samples reported greatest time depths than other samples in results of two of the three methods, namely the Rho and the LD methods. Only in the results of the Selection method, they didn't report the highest age, but they still remained in the top few greatest ages reported.

If anything, the results of Nabil & co. just go to show how LP is largely a natural response to dairy-rich dietary, and as a result, LP has emerged independently as homoplasic events in different areas of the world, on different allelic backgrounds in some cases, and possibly on similar/shared allelic ancestral backgrounds in others, with the latter serving as relics of common ancestry. As matter of fact, there are alleles dramatically different from those available in Europe altogether, that are also linked to LP; to recapitulate:

After testing for lactose tolerance and genetic makeup among 43 ethnic groups in East Africa, she and her colleagues have found three **new** mutations **all independent of one another** and **of the European mutation**, that keep the lactase gene permanently switched on.- New York Times, on the findings of Sarah Tiskhoff and her research team.

While LP trait need not necessarily be confined to pastoralists, it does have a strong correlative-association with pastoralist and heavy dairy-dietary lifestyles. It is inclined to be predominant in pastoralist groups, because they are more likely to be natural milk-consumers than agro-based sedentary communities, who generally dwell on more dietary choices. For example, the contrasts observed in nomadic Fulani vs. sedentary counterparts by Mulcare et al. 2004, where the 13kb T allele was concerned, testify to the possible adaptive property of T allele, as primarily a response to the pastoralist lifestyle of the nomadic Fulani, rather than a function of gene flow from a foreign source into the Fulani gene pool. The nomadic Fulani of the Cameroonian region were reported to have substantial frequency of the T allele, while their sedentary Fulani counterparts only featured very little; this is so, even though both groups shared considerable hg R1* Y-DNA markers.

What does all this mean then? The pastoralist Fulani would have lactase persistent trait with or without receiving LP alleles from an exogenous source; hence, it makes little sense to attribute this trait to European origin. In fact, pastoralism took hold on the African continent long before it did many parts of the world; it is among the earliest practiced anywhere, if not the earliest. So, populations here would have developed lactase persistent long before European communities, who themselves have varying degrees of LP trait. There is reportedly a gradient that shows loss of LP trait as one moves down from northwest Europe to southern Europe. The Funnel Beaker region of northwest Europe has earned a distinction in Europe for having the heaviest concentration of LP bearing communities. There are communities in the southern territories of Europe who are essentially lactose intolerant. It's because the LP trait is an adaptive marker, and cannot conveniently be paired with some uniparental marker considered to be of foreign origin, so as to press for foreign ancestry in a non-European people [like the Fulani], research teams like those of Mulcare, Nabil, and yes, even Malar J. (author of the topmost abstract) et al. felt compelled to call on foreign/external sources, no matter how flimsy those sources themselves may be, as a means to bolster their otherwise fragile theories using either the LP allele or some other imprecise or unpredictable DNA markers.

5 comments:

"There seems to be a trend amongst 'western' geneticists, to cite third party (not of their own) sources to bolster theories that cannot be sufficiently explained by their own findings."

Yes. Putting your own research in the context of the literature in the area is part of what is expected in every scientific publication from a third grader's science fair project to a doctoral dissertation to these kinds of journal articles by established academics. There is nothing wrong with doing that and a failure to reference the literature for the purpose would be considered almost unethical. This is one reasons that supplementary data sets that are publicly available and have well documented methodologies are so important.

Andrew, you should make a habit of reading the full article before you comment on it, which is also expected of any third grader, so that you won't run into avoidable mistakes. The piece you cherry-picked, was actually written in the following context, upon further reading, and please pay attention to the highlighted bits:

There seems to be a trend amongst 'western' geneticists, to cite third party (not of their own) sources to bolster theories that cannot be sufficiently explained by their own findings. This often leads to the referencing of sources that concern samples of geographic specifics, and possibly, sample sizes that are distinct from those of the research group doing the citing [of the foreign source], without full understanding of the archeological record and linguistic background of the sample subjects under study.

The point of this piece being, that researchers often cross-reference without taking additional care to take into consideration the full context under which their referenced external source was achieved, such as the samples sizes, the geographical extent of those samples, the specific demographic components of those samples, etc, that the other researchers whom they are citing were working with; as result, they end up coupling results from two different studies, which would otherwise in actuality be contradictory in their findings, because they would have been made under two different contexts. It is like some author who attempts to use the results of some Lactase persistence allele trait of the Fulani in one external study, and then tries to use that data to support to his/her own theory about the same ethnic group around a totally different locus or marker type--let's say, Y-DNA marker, without taking into consideration the full analytical context of the study the author is referencing. As a result, the author may miss out on the possibility that the lactase persistent allele may not necessarily be predicted by Y-DNA or mtDNA markers, just like Mulcare et al. found out--the hard way. I had also provided a specific example of a researcher trying to cross-reference from another study, and arrived at a dubious conclusion, because the author in question did not carefully consider what the other study was actually relating about Fulani ancestry. That author ended up saying something quite different from the study he referenced. To this end, if you had bothered to read my article in its entirety instead of cherry-picking one line out of context, you would have run into this bit:

they too were compelled to cite an external source, as means to solidify their theory. Citing external sources in of itself is not an unreasonable thing to do; the only problem is that this source does not prove to be that impactive.

In other words, the external source being used, was not doing the deed it was cited to do.

But, the case that R1b in Africa (mostly R-V88 and mostly in Chadic language speakers, a differentiated subtype of R1b not captured by tests geared to Europeans, and not actually bare R-M173 as previously believed which is the haplogroup found in Australia and the Americas), probably introgressed into the African gene pool in Neolithic times is pretty solid. The phylogenetic tree puts the origins of both R1 and R2 in South Asia, with R2 largely staying confined there and R1 splitting into R1a and R1b apparently somewhere in a triangle roughly having Yemen, Iran and Greece as corners, and R1b splitting into European and African branches sometime after that, probably somewhere in between Turkey and Sudan.

You are commenting on topic that was not part of the article you were responding to, but be that as it may, your conclusion about all African R1* markers not including the "bare R-M173" is actually false. Fulani samples studied by Hassan et al. were not R1b, because they did not have the P25 marker, and I'm talking about the full set of R1* chromosomes in those Fulani samples. R1b have the P25 mutation. And don't think about using that line of "P25 may not be stable" or something to that effect. If that were so, the Fulani samples in question could have been expected to have a mix of R1 markers bearing the P25 mutation and those without it. However, all the Sudanese Fulani samples did not have P25.

As for the "phylogenetic tree", whatever they put is conjecture. Upstream clades of hg R, without the established downstream nodes, have also been identified on the African continent. I discuss these matters in detail under another topic, different from the one you were commenting on. I recommend you read it, if you care to.

Y-DNA haplogroup T that is common in a subset of the Fulani, likewise decends from haplogroup F with roots in West Eurasia, not from the A, B, or E haplogroups likely to have origins in Africa, probably making its way to the Sahel via either during a wet Sahara epsisode in the Holocene, down the Nile Valley, or across from the Horn of Africa where it would have arrived by sea, probably sometime before the Chadic speakers arrived.

What are you basing this idea of haplgroup T being common in the Fulani on? I don't recall any study wherein this marker had been identified in the Fulani. What study are you referencing? The lactase-persistent T alleles found in nomadic Fulani are not just found in a single "subset of Fulanis", but in Fulani sampled from different geographical territories. The T allele is not the only lactase-persistent allele amongst the Fulani either.

Is it possible that you could have confused the T allele being discussed in my article with the Y-DNA counterpart? My article was discussing the MCM6 gene lactase-persistence T allele, NOT the Y-DNA.

BUT for the sake of argument, suppose I entertained your idea that Y-DNA "hg T is common in a section of Fulani", then this haplogroup will not necessarily serve as proof of "West Asian" ancestry, as that clade actually has more presence in Africa, eastern Africa to be specific, than "west Asia". Yet those very same eastern African populations which carry hg T, have rare to no lactase-persistance T alleles. That right there, punches a hole in your logic, about the association between hg T and the lactase-persistent T allele variants. It is just as probable that hg T has an eastern African origin, instead of "west Asia". I discussed that matter under another topic as well.

Andrew Oh-Willeke writes:

The fact that some populations independently developed different LP genes further supports the idea that when there is a match with European versions that it has that origin.

This tells me that you indeed had not bothered to read my article. There in I demonstrate how the T alleles common in Europe actually appear and could have emerged independently under different/multiple allelic backgrounds. So, to say that whenever there is a Lactase-persistent T allele, it has got to be of European origin, is a careless comment to make me...disregarding available data. If you disagree, you'd have to tackle the points I raised head on, and point by point with evidence to the contrary.

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